Among the 3 methods used on 478 samples included in the study, next-generation sequencing provided the most favorable results.
As next-generation sequencing (NGS) adoption continues in various diseases and conditions, new research suggests the method is more reliable than traditional detection methods SMN1 gene copy number in patients with spinal muscular atrophy (SMA).
The researchers of the study, published in Scientific reports, said the screening method could offer a simplified way to detect gene copy number without the need for additional testing, and provide high-cost performance, as the study also showed that NGS could reduce the costs of tests.
“It is recommended by the [American College of Obstetrics and Gynecology] and [American College of Medical Genetics] that all women and couples, regardless of race or ethnicity, be screened for carriers of SMA, a serious genetic disease common worldwide,” the researchers emphasized. “Thus, selecting an appropriate method is of vital importance. Therefore, good performance should be the first priority.
Of the 3 methods used in 478 samples included in the study, NGS gave the most favorable results, including when compared to multiplex ligation probe amplification (MLPA), which is generally considered the gold standard. gold for molecular analysis of SMA. According to the researchers, their study is the first to analyze the retest rate of the traditional screening method.
Compared to MLPA (6.69%) and quantitative polymerase chain reaction (qPCR) (5%) – another commonly used method for SMN1 gene copy number screening – NGS had the lowest retest rate at 2.74%, meaning fewer samples had to be retested to get definitive results.
The analysis also demonstrated that NGS had higher precision and specificity. Using classifications determined by the MLPA as a benchmark, which were consistent with previous diagnostic results, researchers tested the ability of NGS and qPCR to identify 0 copies, 1 copies, and ≥ 2 copies of SMN1. On all of these 3 measurements, the NGS demonstrated 100% sensitivity, specificity and precision. Using qPCR, the sensitivity was 100%, 97.52%, and 94.30%, respectively; the specificity was 98.63%, 95.48% and 100% respectively; and the accuracy was 72.72%, 88.72% and 100%, respectively.
Of the samples, 71 were used to determine the repeatability of NGS and qPCR. While reproducibility was sufficient among homozygous deletion samples for qPCR, results were insufficient among heterozygous deletion and non-deletion samples. Meanwhile, NGS showed favorable repeatability, which the researchers say suggests that NGS can be used not only to detect homozygous deletion for SMA diagnosis, but also to analyze heterozygous deletion for screening. carriers.
Besides the 3 methods studied, there are other methods that can be used to SMN1 copy number detection, the researchers wrote. “Droplet-based digital PCR is another emerging technique for SMN1 copy number test. Although improved digital PCR technology has been reported, most are operational complexity and the related equipment and reagents are expensive. At present, it is primarily used as a validation method for positive results and has not been widely adopted for screening SMA carriers,” they concluded.
Zhao S, Wang Y, Xin X, et al. Next-generation sequencing is a very reliable method to analyze deletion of exon 7 of survival motor neuron 1 (SMN1) uncomfortable. Scientific representative. Published online January 7, 2022. doi: 10.1038/s41598-021-04325-1